def test_proper_torsion():
# proper torsions have a variadic number of terms
patterns = [
['[*:1]-[#6X3:2]=[#6X3:3]-[*:4]', [[99., 99., 99.]]],
['[*:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[99., 99., 99.]]],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[1., 2., 3.], [4., 5., 6.]]],
[
'[#35:1]-[#6X3:2]=[#6X3:3]-[#35:4]',
[[7., 8., 9.], [1., 3., 5.], [4., 4., 4.]]
],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#9:4]', [[7., 8., 9.]]],
]
smirks = [x[0] for x in patterns]
params = [x[1] for x in patterns]
props = None
ph = bonded.ProperTorsionHandler(smirks, params, None)
obj = ph.serialize()
all_handlers = deserialize_handlers(bin_to_str(obj))
assert len(all_handlers) == 1
new_ph = all_handlers[0]
np.testing.assert_equal(new_ph.smirks, ph.smirks)
np.testing.assert_equal(new_ph.params, ph.params)
assert new_ph.props == ph.props
def test_proper_torsion():
# proper torsions have a variadic number of terms
patterns = [
['[*:1]-[#6X3:2]=[#6X3:3]-[*:4]', [[99., 99., 99.]]],
['[*:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[99., 99., 99.]]],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[1., 2., 3.], [4., 5., 6.]]],
[
'[#35:1]-[#6X3:2]=[#6X3:3]-[#35:4]',
[[7., 8., 9.], [1., 3., 5.], [4., 4., 4.]]
],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#9:4]', [[7., 8., 9.]]],
]
smirks = [x[0] for x in patterns]
params = [x[1] for x in patterns]
props = None
hbh = bonded.ProperTorsionHandler(smirks, params, props)
mol = Chem.MolFromSmiles("FC(Br)=C(Br)F")
torsion_idxs, (torsion_params, torsion_vjp_fn) = hbh.parameterize(mol)
assert torsion_idxs.shape == (8, 4)
assert torsion_params.shape == (8, 3)
torsion_param_adjoints = np.random.randn(*torsion_params.shape)
ff_adjoints = torsion_vjp_fn(torsion_param_adjoints)[0]
mask = np.argwhere(torsion_params > 90)
assert np.all(ff_adjoints[mask] == 0.0) == True
def test_proper_torsion():
# proper torsions have a variadic number of terms
patterns = [
['[*:1]-[#6X3:2]=[#6X3:3]-[*:4]', [[99., 99., 99.]]],
['[*:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[99., 99., 99.]]],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[1., 2., 3.], [4., 5., 6.]]],
['[#35:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[7., 8., 9.], [1., 3., 5.], [4., 4., 4.]]],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#9:4]', [[7., 8., 9.]]],
]
smirks = [x[0] for x in patterns]
params = [x[1] for x in patterns]
props = None
pth = bonded.ProperTorsionHandler(smirks, params, props)
mol = Chem.MolFromSmiles("FC(Br)=C(Br)F")
torsion_params, torsion_idxs = pth.parameterize(mol)
assert torsion_idxs.shape == (8, 4)
assert torsion_params.shape == (8, 3)
torsion_params_new, torsion_vjp_fn, torsion_idxs_new = jax.vjp(functools.partial(pth.partial_parameterize, mol=mol), pth.params, has_aux=True)
np.testing.assert_array_equal(torsion_params_new, torsion_params)
np.testing.assert_array_equal(torsion_idxs_new, torsion_idxs)
torsion_param_adjoints = np.random.randn(*torsion_params.shape)
ff_adjoints = torsion_vjp_fn(torsion_param_adjoints)[0]
mask = np.argwhere(torsion_params > 90)
assert np.all(ff_adjoints[mask] == 0.0) == True